Closed ifiddes-10x-zz closed 6 years ago
Hi Ian, I've reworked the code for SVanalyzer extensively, and condensed its functionality into five use cases: SVmerge - merge equivalent SVs in one or more VCF files SVcomp - pairs of structural variants (same as previously) SVbenchmark - compare one "test" VCF file to a "truth" VCF file and report precision, recall, f1 SVwiden - characterize structural variants as to similarity at their breakpoints, and thus ambiguity in their positioning SVrefine - call repeat-aware structural variants from assembly alignments (also same as previous versions)
Documentation is at http://svanalyzer.readthedocs.io/en/latest/, and code is considerably cleaner than before. Please give it a try at your convenience!
https://github.com/nhansen/SVanalyzer/blob/master/scripts/SVfindmatches.pl#L81